The ‘aggregation model of coexistence’ predicts that a strong and independent aggregation of species across ephemeral resource patches promotes species coexistence and maintains diversity. This study examines the role of aggregation in maintaining tropical dung beetle diversity and the effects of deforestation on aggregation patterns and diversity loss. Using clusters of pitfall traps, dung beetle aggregation was quantified in natural and disturbed habitat at nested temporal and spatial scales in central Peru. The results indicate that dung was colonized by a greater number of species, many of which were large, leading to a higher total beetle biomass in forest habitat than in deforested, farm habitat. Beetles were intraspecifically aggregated at each spatial scale examined. Habitat-type (forest/deforested) had no effect on the intensity of intra- or interspecific aggregation. Analyses of aggregation patterns revealed that dung beetle assemblages in forest habitat were generally saturated whereas in deforested habitat they were unsaturated. In general, interspecific aggregation was too weak relative to intraspecific aggregation to explain the high diversity of species in forest habitat. Other mechanisms, including resource partitioning are likely to play a greater role in maintaining the diversity of dung beetle assemblages in the region. These results also indicate that the loss of species from disturbed habitat has not been due to a breakdown in the aggregation mechanism.